8.A.46 The Glycan-binding Protein (SusD) Family Bacteroides thetaiotaomicron, a gram-negative obligate anaerobe, utilizes polysaccharides by binding them to its cell surface and allowing cell-associated enzymes to hydrolyze them into digestible fragments. Reeves et al. 1997 used the starch utilization system as a model to analyze the initial steps involved in polysaccharide binding and breakdown. ¹⁴C-Starch binding assays showed that SusC and SusD both contribute to starch binding, that SusC and SusD interact in the outer membrane, and that they are exposed to the cell surface. Koropatkin et al. 2009 presented the atomic structure of the B. thetaiotaomicron protein BT1043, an outer membrane lipoprotein involved in host glycan metabolism that is a structural homologue of the B. thetaiotaomicron starch-binding protein SusD. Both structures are dominated by tetratrico peptide repeats that may facilitate association with outer membrane beta-barrel transporters required for glycan uptake. The structure of BT1043 complexed with N-acetyllactosamine revealed that recognition is mediated via hydrogen bonding interactions with the reducing end of beta-N-acetylglucosamine, suggesting a role in binding glycans liberated from the mucin polypeptide. The glycan-binding pocket of BT1043 suggests that binding of ligands to BT1043 relies more upon interactions with the composite sugar residues than upon overall ligand conformation as previously observed for SusD. The diversity in amino acid sequence level likely reflects early divergence from a common ancestor, while the unique and conserved alpha-helical fold the SusD family suggests a similar function in glycan uptake.
References:
Bakolitsa, C., Q. Xu, C.L. Rife, P. Abdubek, T. Astakhova, H.L. Axelrod, D. Carlton, C. Chen, H.J. Chiu, T. Clayton, D. Das, M.C. Deller, L. Duan, K. Ellrott, C.L. Farr, J. Feuerhelm, J.C. Grant, A. Grzechnik, G.W. Han, L. Jaroszewski, K.K. Jin, H.E. Klock, M.W. Knuth, P. Kozbial, S.S. Krishna, A. Kumar, W.W. Lam, D. Marciano, D. McMullan, M.D. Miller, A.T. Morse, E. Nigoghossian, A. Nopakun, L. Okach, C. Puckett, R. Reyes, H.J. Tien, C.B. Trame, H. van den Bedem, D. Weekes, K.O. Hodgson, J. Wooley, M.A. Elsliger, A.M. Deacon, A. Godzik, S.A. Lesley, and I.A. Wilson. (2010). Structure of BT_3984, a member of the SusD/RagB family of nutrient-binding molecules. Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 1274-1280.
Cho, K.H. and A.A. Salyers. (2001). Biochemical analysis of interactions between outer membrane proteins that contribute to starch utilization by Bacteroides thetaiotaomicron. J. Bacteriol. 183: 7224-7230.
Curtis, M.A., S.A. Hanley, and J. Aduse-Opoku. (1999). The rag locus of Porphyromonas gingivalis: a novel pathogenicity island. J Periodontal Res 34: 400-405.
Goulas, T., I.G. Ferrer, J.A. Hutcherson, B.A. Potempa, J. Potempa, D.A. Scott, and F.X. Gomis-Rüth. (2015). Structure of RagB, a major immunodominant outer-membrane surface receptor antigen of Porphyromonas gingivalis. Mol Oral Microbiol. [Epub: Ahead of Print]
Koropatkin, N., E.C. Martens, J.I. Gordon, and T.J. Smith. (2009). Structure of a SusD homologue, BT1043, involved in mucin O-glycan utilization in a prominent human gut symbiont. Biochemistry 48: 1532-1542.
Phansopa C., Roy S., Rafferty JB., Douglas CW., Pandhal J., Wright PC., Kelly DJ. and Stafford GP. (2014). Structural and functional characterization of NanU, a novel high-affinity sialic acid-inducible binding protein of oral and gut-dwelling Bacteroidetes species. Biochem J. 458(3):499-511.
Reeves, A.R., G.R. Wang, and A.A. Salyers. (1997). Characterization of four outer membrane proteins that play a role in utilization of starch by Bacteroides thetaiotaomicron. J. Bacteriol. 179: 643-649.
Shipman, J.A., J.E. Berleman, and A.A. Salyers. (2000). Characterization of four outer membrane proteins involved in binding starch to the cell surface of Bacteroides thetaiotaomicron. J. Bacteriol. 182: 5365-5372.
Examples:
TC#	Name	Organismal Type	Example
8.A.46.1.1	*SusD starch and maltooligosaccharide-binding protein of 551 aas. Functions in a complex with SusC OM Receptor (TC# 1.B.14.6.1) (Shipman et al.* 2000; Reeves et al. 1997; Cho and Salyers 2001).**	Bacteroidetes	SusD of Bacteroides thetaiotaomicron

8.A.46.1.2	SusD/RagB domain-containing protein of 501 aas.	Bacteroidetes	SusD homologue of Odoribacter splanchnicus

8.A.46.1.3	SusD/RagB homologue of 603 aas.	Bacteroidetes	SusD homologue of Pedobacter heparinus

8.A.46.1.4	*High affinity sialic acid binding protein, NanU of 516 aas with an N-terminal TMS and 17 putative β-strands. The 3-d structure is known (Phansopa et al.* 2013).**	Bacteroidetes	NanU of Bacteroides fragilis

8.A.46.1.5	SusD/RagB domain protein of 545 aas.	Bacteroidetes	SusD homolgoue of Leadbetterella byssophila

8.A.46.1.6	RegB homologue of 572 aas	Bacteroidetes	RegB homologue of Cyclobacterium marinum (Flectobacillus marinus)

Examples:
TC#	Name	Organismal Type	Example
8.A.46.2.1	SusD homologue. Functions with SusC homologue, TC# 1.B.14.6.13.	Bacteroidetes	SusD homologue of Bacteroides thetaiotaomicron

8.A.46.2.2	*SusD homologue of 537 aas. The 3-d structure is known to 1.7 Å resolution (Bakolitsa et al.* 2010).**	Bacteroidetes	BT_3984 protein of Bacteroides thetaiotaomicron

8.A.46.2.3	RegB homologue of 571 aas	Bacteroidetes	RegB homologue of Muricauda ruestringensis

Examples:
TC#	Name	Organismal Type	Example
8.A.46.3.1	RagB of 501 aas, outer membrane sugar-binding lipoprotein similar in structure to Bacteroides thetaiotaomicron SusD and Tannerella forsythia NanU which are respectively involved in maltooligosaccharide and sialic acid binding and uptake (Goulas et al. 2015).		RagB of Porphyromonas gingivalis

8.A.46.3.2	SusD family protein of 504 aas		SusD protein of Bacteroides fluxus

8.A.46.3.3	RagB/SusD domain-containing protein of 502 aas		RagB of Niastella koreensis

8.A.46.3.4	SusD homologue of 674 aas and 1 N-terminal TMS.		SusD of Bacteroides fragilis

8.A.46.3.5	*RagB of 503 aas; acts in concert with RagA (TC# 1.B.14.6.16), both encoded within a single operon (Curtis et al.* 1999).**		RagB of Porphyromonas gingivalis